rs11833537

Variant names:

• chr12-4170941-T-C
• rs11833537

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.336 in 152,092 control chromosomes in the GnomAD database, including 9,260 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51080 AN: 151972 Hom.: 9259 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.323

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.336 AC: 51094 AN: 152092 Hom.: 9260 Cov.: 32 AF XY: 0.334 AC XY: 24856 AN XY: 74338

African (AFR) AF: 0.218 AC: 9025 AN: 41494

American (AMR) AF: 0.316 AC: 4826 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1284 AN: 5158

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4624 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27732 AN: 67992

Other (OTH) AF: 0.320 AC: 675 AN: 2110

Alfa AF: 0.379 Hom.: 45490

Bravo AF: 0.317

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.71
PhyloP100		0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11833537; hg19: chr12-4280107;